Evolution Requires Reproduction Variation and Selective Pressure

I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Once the necessary building blocks were available, how did a living system arise and evolve? Before the appearance of
life, simple molecular systems must have existed that subsequently evolved into the complex chemical systems that are
characteristic of organisms. To address how this evolution occurred, we need to consider the process of evolution. There
are several basic principles common to evolving systems, whether they are simple collections of molecules or competing
populations of organisms. First, the most fundamental property of evolving systems is their ability to replicate or
reproduce. Without this ability of reproduction, each "species" of molecule that might appear is doomed to extinction as
soon as all its individual molecules degrade. For example, individual molecules of biological polymers such as
ribonucleic acid are degraded by hydrolysis reactions and other processes. However, molecules that can replicate will
continue to be represented in the population even if the lifetime of each individual molecule remains short.
A second principle fundamental to evolution is variation. The replicating systems must undergo changes. After all, if a
system always replicates perfectly, the replicated molecule will always be the same as the parent molecule. Evolution
cannot occur. The nature of these variations in living systems are considered in Section 2.2.5.
A third basic principle of evolution is competition. Replicating molecules compete with one another for available
resources such as chemical precursors, and the competition allows the process of evolution by natural selection to occur.
Variation will produce differing populations of molecules. Some variant offspring may, by chance, be better suited for
survival and replication under the prevailing conditions than are their parent molecules. The prevailing conditions exert a
selective pressure that gives an advantage to one of the variants. Those molecules that are best able to survive and to
replicate themselves will increase in relative concentration. Thus, new molecules arise that are better able to replicate
under the conditions of their environment. The same principles hold true for modern organisms. Organisms reproduce,
show variation among individual organisms, and compete for resources; those variants with a selective advantage will
reproduce more successfully. The changes leading to variation still take place at the molecular level, but the selective
advantage is manifest at the organismal level.
2.2.1. The Principles of Evolution Can Be Demonstrated in Vitro
Is there any evidence that evolution can take place at the molecular level? In 1967, Sol Spiegelman showed that
replicating molecules could evolve new forms in an experiment that allowed him to observe molecular evolution in the
test tube. He used as his evolving molecules RNA molecules derived from a bacterial virus called bacteriophage Q β .
The genome of bacteriophage Q β , a single RNA strand of approximately 3300 bases, depends for its replication on the
activity of a protein complex termed Q β replicase. Spiegelman mixed the replicase with a starting population of Q β
RNA molecules. Under conditions in which there are ample amounts of precursors, no time constraints, and no other
selective pressures, the composition of the population does not change from that of the parent molecules on replication.
When selective pressures are applied, however, the composition of the population of molecules can change dramatically.
For example, decreasing the time available for replication from 20 minutes to 5 minutes yielded, incrementally over 75
generations, a population of molecules dominated by a single species comprising only 550 bases. This species is
replicated 15 times as rapidly as the parental Q β RNA (Figure 2.4). Spiegelman applied other selective pressures by, for
example, limiting the concentrations of precursors or adding compounds that inhibit the replication process. In each case,
new species appeared that replicated more effectively under the conditions imposed.
The process of evolution demonstrated in these studies depended on the existence of machinery for the replication of
RNA fragments in the form of the Q β replicase. As noted in Chapter 1, one of the most elegant characteristics of nucleic
acids is that the mechanism for their replication follows naturally from their molecular structure. This observation
suggests that nucleic acids, perhaps RNA, could have become self-replicating. Indeed, the results of studies have
revealed that single-stranded nucleic acids can serve as templates for the synthesis of their complementary strands and
that this synthesis can occur spontaneously that is, without biologically derived replication machinery. However,
investigators have not yet found conditions in which an RNA molecule is fully capable of independent selfreplication
from simple starting materials.
2.2.2. RNA Molecules Can Act As Catalysts
The development of capabilities beyond simple replication required the generation of specific catalysts. A catalyst is a
molecule that accelerates a particular chemical reaction without itself being chemically altered in the process. The
properties of catalysts will be discussed in detail in Chapters 8 and 9. Some catalysts are highly specific; they promote
certain reactions without substantially affecting closely related processes. Such catalysts allow the reactions of specific
pathways to take place in preference to those of potential alternative pathways. Until the 1980s, all biological catalysts,
termed enzymes, were believed to be proteins. Then, Tom Cech and Sidney Altman independently discovered that certain
RNA molecules can be effective catalysts. These RNA catalysts have come to be known as ribozymes. The discovery of
ribozymes suggested the possibility that catalytic RNA molecules could have played fundamental roles early in the
evolution of life.
The catalytic ability of RNA molecules is related to their ability to adopt specific yet complex structures. This principle
is illustrated by a "hammerhead" ribozyme, an RNA structure first identified in plant viruses (Figure 2.5). This RNA
molecule promotes the cleavage of specific RNA molecules at specific sites; this cleavage is necessary for certain
aspects of the viral life cycle. The ribozyme, which requires Mg2+ ion or other ions for the cleavage step to take place,
forms a complex with its substrate RNA molecule that can adopt a reactive conformation.
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The existence of RNA molecules that possess specific binding and catalytic properties makes plausible the idea of an
early "RNA world" inhabited by life forms dependent on RNA molecules to play all major roles, including those
important in heredity, the storage of information, and the promotion of specific reactions that is, biosynthesis and
energy metabolism.
2.2.3. Amino Acids and Their Polymers Can Play Biosynthetic and Catalytic Roles
In the early RNA world, the increasing populations of replicating RNA molecules would have consumed the building
blocks of RNA that had been generated over long periods of time by prebiotic reactions. A shortage of these compounds
would have favored the evolution of alternative mechanisms for their synthesis. A large number of pathways are
possible. Examining the biosynthetic routes utilized by modern organisms can be a source of insight into which
pathways survived. A striking observation is that simple amino acids are used as building blocks for the RNA bases
(Figure 2.6). For both purines (adenine and guanine) and pyrimidines (uracil and cytosine), an amino acid serves as a
core onto which the remainder of the base is elaborated. In addition, nitrogen atoms are donated by the amino group of
the amino acid aspartic acid and by the amide group of the glutamine side chain.
Amino acids are chemically more versatile than nucleic acids because their side chains carry a wider range of chemical
functionality. Thus, amino acids or short polymers of amino acids linked by peptide bonds, called polypeptides (Figure
2.7), may have functioned as components of ribozymes to provide a specific reactivity. Furthermore, longer polypeptides
are capable of spontaneously folding to form well-defined three-dimensional structures, dictated by the sequence of
amino acids along their polypeptide chains. The ability of polypeptides to fold spontaneously into elaborate structures,
which permit highly specific chemical interactions with other molecules, may have favored the expansion of their roles
in the course of evolution and is crucial to their dominant position in modern organisms. Today, most biological catalysts
(enzymes) are not nucleic acids but are instead large polypeptides called proteins.
2.2.4. RNA Template-Directed Polypeptide Synthesis Links the RNA and Protein
Worlds
Polypeptides would have played only a limited role early in the evolution of life because their structures are not suited to
self-replication in the way that nucleic acid structures are. However, polypeptides could have been included in
evolutionary processes indirectly. For example, if the properties of a particular polypeptide favored the survival and
replication of a class of RNA molecules, then these RNA molecules could have evolved ribozyme activities that
promoted the synthesis of that polypeptide. This method of producing polypeptides with specific amino acid sequences
has several limitations. First, it seems likely that only relatively short specific polypeptides could have been produced in
this manner. Second, it would have been difficult to accurately link the particular amino acids in the polypeptide in a
reproducible manner. Finally, a different ribozyme would have been required for each polypeptide. A critical point in
evolution was reached when an apparatus for polypeptide synthesis developed that allowed the sequence of bases in an
RNA molecule to directly dictate the sequence of amino acids in a polypeptide. A code evolved that established a relation
between a specific sequence of three bases in RNA and an amino acid. We now call this set of three-base combinations,
each encoding an amino acid, the genetic code. A decoding, or translation, system exists today as the ribosome and
associated factors that are responsible for essentially all polypeptide synthesis from RNA templates in modern
organisms. The essence of this mode of polypeptide synthesis is illustrated in Figure 2.8.
An RNA molecule (messenger RNA, or mRNA), containing in its base sequence the information that specifies a particular
protein, acts as a template to direct the synthesis of the polypeptide. Each amino acid is brought to the template attached
to an adapter molecule specific to that amino acid. These adapters are specialized RNA molecules (called transfer RNAs
or tRNAs). After initiation of the polypeptide chain, a tRNA molecule with its associated amino acid binds to the
template through specific Watson-Crick base-pairing interactions. Two such molecules bind to the ribosome and peptidebond formation is catalyzed by an RNA component (called ribosomal RNA or rRNA) of the ribosome. The first RNA
departs (with neither the polypeptide chain nor an amino acid attached) and another tRNA with its associated amino acid
bonds to the ribosome. The growing polypeptide chain is transferred to this newly bound amino acid with the formation
of a new peptide bond. This cycle then repeats itself. This scheme allows the sequence of the RNA template to encode
the sequence of the polypeptide and thereby makes possible the production of long polypeptides with specified
sequences. The mechanism of protein synthesis will be discussed in Chapter 29. Importantly, the ribosome is composed
largely of RNA and is a highly sophisticated ribozyme, suggesting that it might be a surviving relic of the RNA world.
2.2.5. The Genetic Code Elucidates the Mechanisms of Evolution
The sequence of bases that encodes a functional protein molecule is called a gene. The genetic code that is, the relation
between the base sequence of a gene and the amino acid sequence of the polypeptide whose synthesis the gene
directs applies to all modern organisms with only very minor exceptions. This universality reveals that the genetic
code was fixed early in the course of evolution and has been maintained to the present day.
We can now examine the mechanisms of evolution. Earlier, we considered how variation is required for evolution. We
can now see that such variations in living systems are changes that alter the meaning of the genetic message. These
variations are called mutations. A mutation can be as simple as a change in a single nucleotide (called a point mutation),
such that a sequence of bases that encoded a particular amino acid may now encode another (Figure 2.9A). A mutation
can also be the insertion or deletion of several nucleotides.
Other types of alteration permit the more rapid evolution of new biochemical activities. For instance, entire sections of
the coding material can be duplicated, a process called gene duplication (Figure 2.9B). One of the duplication products
may accumulate mutations and eventually evolve into a gene with a different, but related, function. Furthermore, parts of
a gene may be duplicated and added to parts of another to give rise to a completely new gene, which encodes a protein
with properties associated with each parent gene. Higher organisms contain many large families of enzymes and other
macromolecules that are clearly related to one another in the same manner. Thus, gene duplication followed by
specialization has been a crucial process in evolution. It allows the generation of macromolecules having particular
functions without the need to start from scratch. The accumulation of genes with subtle and large differences allows for
the generation of more complex biochemical processes and pathways and thus more complex organisms.
2.2.6. Transfer RNAs Illustrate Evolution by Gene Duplication
Transfer RNA molecules are the adaptors that associate an amino acid with its correct base sequence. Transfer RNA
molecules are structurally similar to one another: each adopts a three-dimensional cloverleaf pattern of base-paired
groups (Figure 2.10). Subtle differences in structure enable the protein-synthesis machinery to distinguish transfer RNA
molecules with different amino acid specificities.
This family of related RNA molecules likely was generated by gene duplication followed by specialization. A nucleic
acid sequence encoding one member of the family was duplicated, and the two copies evolved independently to generate
molecules with specificities for different amino acids. This process was repeated, starting from one primordial transfer
RNA gene until the 20 (or more) distinct members of the transfer RNA family present in modern organisms arose.
2.2.7. DNA Is a Stable Storage Form for Genetic Information
It is plausible that RNA was utilized to store genetic information early in the history of life. However, in modern
organisms (with the exception of some viruses), the RNA derivative DNA (deoxyribonucleic acid) performs this function
(Sections 1.1.1 and 1.1.3). The 2 -hydroxyl group in the ribose unit of the RNA backbone is replaced by a hydrogen atom
in DNA (Figure 2.11).
What is the selective advantage of DNA over RNA as the genetic material? The genetic material must be extremely
stable so that sequence information can be passed on from generation to generation without degradation. RNA itself is a
remarkably stable molecule; negative charges in the sugar-phosphate backbone protect it from attack by hydroxide ions
that would lead to hydrolytic cleavage. However, the 2 -hydroxyl group makes the RNA susceptible to base-catalyzed
hydrolysis. The removal of the 2 -hydroxyl group from the ribose decreases the rate of hydrolysis by approximately 100fold under neutral conditions and perhaps even more under extreme conditions. Thus, the conversion of the genetic
material from RNA into DNA would have substantially increased its chemical stability.
The evolutionary transition from RNA to DNA is recapitulated in the biosynthesis of DNA in modern organisms. In all
cases, the building blocks used in the synthesis of DNA are synthesized from the corresponding building blocks of RNA
by the action of enzymes termed ribonucleotide reductases. These enzymes convert ribonucleotides (a base and
phosphate groups linked to a ribose sugar) into deoxyribonucleotides (a base and phosphates linked to deoxyribose
sugar).
The properties of the ribonucleotide reductases vary substantially from species to species, but evidence suggests that they
have a common mechanism of action and appear to have evolved from a common primordial enzyme.
The covalent structures of RNA and DNA differ in one other way. Whereas RNA contains uracil, DNA contains a
methylated uracil derivative termed thymine. This modification also serves to protect the integrity of the genetic
sequence, although it does so in a less direct manner. As we will see in Chapter 27, the methyl group present in thymine
facilitates the repair of damaged DNA, providing an additional selective advantage.
Although DNA replaced RNA in the role of storing the genetic information, RNA maintained many of its other
functions. RNA still provides the template that directs polypeptide synthesis, the adaptor molecules, the catalytic activity
of the ribosomes, and other functions. Thus, the genetic message is transcribed from DNA into RNA and then translated
into protein.
This flow of sequence information from DNA to RNA to protein (to be considered in detail in Chapters 5, 28, and 29)
applies to all modern organisms (with minor exceptions for certain viruses).
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.4. Evolution in a Test Tube. Rapidly replicating species of RNA molecules were generated from Q β RNA by
exerting selective pressure. The green and blue curves correspond to species of intermediate size that accumulated and
then became extinct in the course of the experiment.
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.5. Catalytic RNA. (A) The base-pairing pattern of a "hammerhead" ribozyme and its substrate. (B) The folded
conformation of the complex. The ribozyme cleaves the bond at the cleavage site. The paths of the nucleic acid
backbones are highlighted in red and blue.
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.6. Biosynthesis of RNA Bases. Amino acids are building blocks for the biosynthesis of purines and
pyrimidines.
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.7. An Alternative Functional Polymer. Proteins are built of amino acids linked by peptide bonds.
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.8. Linking the RNA and Protein Worlds. Polypeptide synthesis is directed by an RNA template. Adaptor
RNA molecules, with amino acids attached, sequentially bind to the template RNA to facilitate the formation of a
peptide bond between two amino acids. The growing polypeptide chain remains attached to an adaptor RNA until the
completion of synthesis.
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.9. Mechanisms of Evolution. A change in a gene can be (A) as simple as a single base change or (B) as
dramatic as partial or complete gene duplication.
I. The Molecular Design of Life
2. Biochemical Evolution
2.2. Evolution Requires Reproduction, Variation, and Selective Pressure
Figure 2.10. Cloverleaf Pattern of tRNA. The pattern of base-pairing interactions observed for all transfer RNA
molecules reveals that these molecules had a common evolutionary origin.